Manuel Holtgrewe
Bioinformatician
Mainz, Rhineland-Palatinate, Germany
Summary
🤩
Rockstar🎓
Top SchoolManuel Holtgrewe is a bioinformatician and software engineering leader with 15+ years designing scalable genomics pipelines and data platforms that have processed 5,000+ exomes/genomes and 200+ TB of data, contributing to 50+ scientific publications. He blends rigorous academic training (PhD, habilitation work in bioinformatics) with hands-on systems engineering, leading agile teams across core bioinformatics units, HPC, and clinical genetics. Manuel is an experienced open-source contributor and DevOps engineer—his work spans rust-bio (complete HMM implementation), Snakemake, SeqAn, and Bioconda—bridging low-level algorithmics and production workflow reliability. Colleagues recognize him for strategic technical leadership, methodological rigor, and a talent for mentoring teams to grow with him. Based in Mainz and Berlin, he actively translates machine learning, statistical methods, and software architecture into diagnostic-grade tools for rare disease genetics. He’s a lifelong learner who combines transistor-level curiosity with biomedical insight to solve impactful problems.
15 years of coding experience
14 years of employment as a software developer
Doctor of Philosophy (PhD), Bioinformatics, Doctor of Philosophy (PhD), Bioinformatics at Freie Universität BerlinHabilitation, Bioinformatik, Habilitation, Bioinformatik at Charité - Universitätsmedizin BerlinDipl.-Inform., Computer Science, Dipl.-Inform., Computer Science at Karlsruhe Institute of Technology (KIT)
German, English
Github Skills (24)
algorithm10
algorithms10
c-language10
package-management10
python10
cluster-computing10
bash10
conda10
sequence-alignment10
data-structure10
data-structures10
bioinformatics10
workflow-management10
rust10
cprogramming-language10
Programming languages (23)
Github contributions (5)
seqan/seqan
Nov 2013 - Aug 2016
SeqAn's official repository.
Role in this project:
Back-end Developer
Back-end DeveloperContributions:734 commits, 13 PRs, 2 pushes in 2 years 9 months
Contributions summary:Manuel's commits primarily focused on fixing issues within the SeqAn library, specifically addressing problems related to incorrect position calculations and type ambiguities. They implemented improvements to existing functionalities by refining code related to interval tree traversal, GFF/GTF file parsing, and the handling of genomic regions. The user also contributed to optimizing the I/O aspects of the code by fixing errors in stream processing for SAM/BAM formats.
simdsequenceindexingsequence-alignmentsseqan
snakemake/snakemake
Nov 2015 - Jun 2022
This is the development home of the workflow management system Snakemake. For general information, see
Role in this project:Back-end Developer & DevOps Engineer
Back-end Developer & DevOps EngineerContributions:6 reviews, 24 commits, 6 PRs in 6 years 8 months
Contributions summary:Manuel primarily contributed to the development and maintenance of the Snakemake workflow management system. Their work included implementing features such as expanding file names for dynamic branches, allowing methods for functions, and using `inspect.isfunction` and `inspect.isfile`. Moreover, the user enhanced the system's resilience by addressing issues such as DRMAA exceptions and rate-limiting cluster job creation. Finally, they made improvements related to cluster job management.
management-systemworkflow-management-systemgeneral-informationreproducibilitysnakemake
Find and Hire Top DevelopersWe’ve analyzed the programming source code of over 60 million software developers on GitHub and scored them by 50,000 skills. Sign-up on Prog,AI to search for software developers.